But this only holds true while the defenses are up. Once you've depleted said defenses, and there is only "internal" left, are all weapons equal? I'm trying to create an "end of the road cleaner upper turret" dedicated to killing stuff that is out of armor.

Am I supposed to just look for the weapon with the highest DPS? Or are some weapons better than others?

In particular flame throwers: They get something like +100% vs internal, but they kind of suck to begin with.

There are also augmentations that affect internal damage, so you should be putting those on your clean-up units :D, but yes, some weapons are better than others, the shotgun is even better than flamethrowers at internal damage.

Also be aware that DPS is not as simple as it might seem, because of the differing ammo storage and reloading times for the various weapons. So for example, you can have a weapon with a great general DPS, but if it only has 10 shots before reloading, and reloading takes twenty minutes, you are better off with a bow and arrow :D

I found that Assault Rifle-wielding troops and various machine gun turrets are best for mop-up of most units, and missiles do work great on larger targets for mopup. I recently got the missiles and they're beast for dealing with mech and tank internals :3